tfbs::patterngen::simplepfm(3pm) [debian man page]
TFBS::PatternGen::SimplePFM(3pm) User Contributed Perl Documentation TFBS::PatternGen::SimplePFM(3pm)NAME
TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory
SYNOPSIS
my @sequences = qw( AAGCCT AGGCAT AAGCCT
AAGCCT AGGCAT AGGCCT
AGGCAT AGGTTT AGGCAT
AGGCCT AGGCCT );
my $patterngen =
TFBS::PatternGen::SimplePFM->new(-seq_list=>@sequences);
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be
passed either as strings, as Bio::Seq objects or as a fasta file.
This pattern generator always creates only one pattern from a given set of sequences.
new
Title : new
Usage : my $db = TFBS::PatternGen::SimplePFM->new(%args);
Function: the constructor for the TFBS::PatternGen::SimplePFM
object
Returns : a TFBS::PatternGen::SimplePFM obkect
Args : This method takes named arguments;
you must specify one of the following
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
pattern
all_patterns
patternSet
The three above methods are used fro the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::SimplePFM(3pm)
Check Out this Related Man Page
TFBS::PatternGen::YMF(3pm) User Contributed Perl Documentation TFBS::PatternGen::YMF(3pm)NAME
TFBS::PatternGen::MEME - a pattern factory that uses the MEME program
SYNOPSIS
my $patterngen =
TFBS::PatternGen::MEME->new(-seq_file=>'sequences.fa',
-binary => 'meme'
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::MEME builds position frequency matrices using an external program MEME written by Bailey and Elkan. For information and
source code of MEME see
http://www.sdsc.edu/MEME
FEEDBACK
Please send bug reports and other comments to the author.
AUTHOR - Wynand Alkema
Wynand Alkema <Wynand.Alkema@cgb.ki.se>
new
Title : new
Usage : my $patterngen = TFBS::PatternGen::YMF->new(%args);
Function: the constructor for the TFBS::PatternGen::MEME object
Returns : a TFBS::PatternGen::MEME object
Args : This method takes named arguments;
you must specify one of the following three
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
Other arguments are:
-binary # a fully qualified path to the 'meme' executable
# OPTIONAL: default 'meme'
-additional_params # a string containing additional
# command-line switches for the
# meme program
pattern
all_patterns
patternSet
The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::YMF(3pm)
Hi,
I'm in need of creating a file in the fasta format:
>1A6A.A
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN
VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR
VEHWGLDEPLLKHWEF
>1A6A.B ... (5 Replies)
If I have a file with the following information
And I would like to remove all the sequences with Freq less than 3, so I end up having the following file:
I am currently using awk to accomplish this task but I am not getting the results I actually want.
Any help will be greatly appreciated. (3 Replies)
Hey everyone,
I would really appreciate some help with a problem I have filing away some data I have. I have multiple fasta files that have different pieces of information in each. I want to split each file into parts, and then file away each separate part into its own file. Here is an example... (8 Replies)
Hi,
I have a folder that contains many (multiple) files
1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files
Each such file have data in the following format
for example:
vi 1.fasta
Code:
>AB_1
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM (6 Replies)
Hi,
I have a folder that contains many (multiple) files
1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files
Each such file have data in the following format
for example:
vi 1.fasta
>AB_1 200bp
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM... (4 Replies)
Hi,
I have a folder that contains many (multiple) files
1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files
Each such file have data in the following format
for example:
vi 1.fasta
58 390
A
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA (7 Replies)
Hello every body ! I'm a new in this forum and beginner in Perl scripting and I have some problems :(:(:(! I have a big file like that :
ID1 ID2 Identity
chromosome07_194379 chromosome01_168057 0.975
chromosome01_100293 chromosome01_168057 ... (23 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
Hi all,
I have a fasta file of a reference sequnce, I will like to retrieve sequences corresponding to a list of start and end position in another file
>my_ref_seq
GCCCTATAAGGGCAGAAGCTTGTCCTTCTTGTGCCAGTTATGACGTTTGTCCTAACTGCACATCTGGTAG... (4 Replies)
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
I need to rename the gene1.fasta file based on the sequence position specified in list.txt as follows,
list.txt
position1=org5... (5 Replies)
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)